Sperm whale population structure in the eastern and central North Pacific inferred by the use of single-nucleotide polymorphisms, microsatellites and mitochondrial DNA

Evidence for seasonal migration by a cryptic top predator of the deep sea

BACKGROUND

In ecosystems influenced by strong seasonal variation in insolation, the fitness of diverse taxa depends on seasonal movements to track resources along latitudinal or elevational gradients. Deep pelagic ecosystems, where sunlight is extremely limited, represent Earth's largest habitable space and yet ecosystem phenology and effective animal movement strategies in these systems are little understood. Sperm whales (Physeter macrocephalus) provide a valuable acoustic window into this world: the echolocation clicks they produce while foraging in the deep sea are the loudest known biological sounds on Earth and convey detailed information about their behavior.

METHODS

We analyze seven years of continuous passive acoustic observations from the Central California Current System, using automated methods to identify both presence and demographic information from sperm whale echolocation clicks. By integrating empirical results with individual-level movement simulations, we test hypotheses about the movement strategies underlying sperm whales' long-distance movements in the Northeast Pacific.

RESULTS

We detect foraging sperm whales of all demographic groups year-round in the Central California Current System, but also identify significant seasonality in frequency of presence. Among several previously hypothesized movement strategies for this population, empirical acoustic observations most closely match simulated results from a population undertaking a "seasonal resource-tracking migration", in which individuals move to track moderate seasonal-latitudinal variation in resource availability.

DISCUSSION

Our findings provide evidence for seasonal movements in this cryptic top predator of the deep sea. We posit that these seasonal movements are likely driven by tracking of deep-sea resources, based on several lines of evidence: (1) seasonal-latitudinal patterns in foraging sperm whale detection across the Northeast Pacific; (2) lack of demographic variation in seasonality of presence; and (3) the match between simulations of seasonal resource-tracking migration and empirical results. We show that sperm whales likely track oceanographic seasonality in a manner similar to many surface ocean predators, but with dampened seasonal-latitudinal movement patterns. These findings shed light on the drivers of sperm whales' long-distance movements and the shrouded phenology of the deep-sea ecosystems in which they forage.

Sperm whale demographics in the Gulf of Alaska and Bering Sea/Aleutian Islands: An overlooked female habitat

Sperm whales exhibit sexual dimorphism and sex-specific latitudinal segregation. Females and their young form social groups and are usually found in temperate and tropical latitudes, while males forage at higher latitudes. Historical whaling data and rare sightings of social groups in high latitude regions of the North Pacific, such as the Gulf of Alaska (GOA) and Bering Sea/Aleutian Islands (BSAI), suggest a more complex distribution than previously understood. Sperm whales are the most sighted and recorded cetacean in marine mammal surveys in these regions but capturing their demographic composition and habitat use has proven challenging. This study detects sperm whale presence using passive acoustic data from seven sites in the GOA and BSAI from 2010 to 2019. Differences in click characteristics between males and females (i.e., inter-click and inter-pulse interval) was used as a proxy for animal size/sex to derive time series of animal detections. Generalized additive models with generalized estimation equations demonstrate how spatiotemporal patterns differ between the sexes. Social groups were present at all recording sites with the largest relative proportion at two seamount sites in the GOA and an island site in the BSAI. We found that the seasonal patterns of presence varied for the sexes and between the sites. Male presence was highest in the summer and lowest in the winter, conversely, social group peak presence was in the winter for the BSAI and in the spring for the GOA region, with the lowest presence in the summer months. This study demonstrates that social groups are not restricted to lower latitudes and capture their present-day habitat use in the North Pacific. It highlights that sperm whale distribution is more complex than accounted for in management protocol and underscores the need for improved understanding of sperm whale demographic composition to better understand the impacts of increasing anthropogenic threats, particularly climate change.

Life History Traits of Sperm Whales Physeter macrocephalus Linnaeus, 1758 Stranded along Italian Coasts (Cetartiodactyla: Physeteridae)

We investigated the relationship between age and body length, and age at sexual maturity of Physeter macrocephalus individuals stranded along the Italian coast. Our molecular analysis shows that all our samples belong to the C.001.002 haplotype, shared between Atlantic and Mediterranean populations. We show that males attain sexual maturity at 10 years, similar to those from other marine areas. However, considering the same body length class, Mediterranean males are older than Atlantic ones. Our finding of a Mediterranean pregnant female of only 6.5 m in length and an assessed age of 24-26 years is particularly noteworthy, considering that females reach sexual maturity at about 9 years and 9 m of total length in other regions. Comparing our results with the literature data, we highlight the positive correlation between lifespan, adult body length and weight of males from the Mediterranean and Atlantic Ocean. Regardless of whether the relatively small size of Mediterranean specimens is a consequence of an inbreeding depression or an adaptation to less favorable trophic conditions, we recommend to closely monitor this population from a conservation perspective. In fact, its low genetic diversity likely corresponds to a relatively limited ability to respond to environmental changes compared with other populations.

Low-coverage reduced representation sequencing reveals subtle within-island genetic structure in Aldabra giant tortoises

Aldabrachelys gigantea (Aldabra giant tortoise) is one of only two giant tortoise species left in the world and survives as a single wild population of over 100,000 individuals on Aldabra Atoll, Seychelles. Despite this large current population size, the species faces an uncertain future because of its extremely restricted distribution range and high vulnerability to the projected consequences of climate change. Captive-bred A. gigantea are increasingly used in rewilding programs across the region, where they are introduced to replace extinct giant tortoises in an attempt to functionally resurrect degraded island ecosystems. However, there has been little consideration of the current levels of genetic variation and differentiation within and among the islands on Aldabra. As previous microsatellite studies were inconclusive, we combined low-coverage and double-digest restriction-associated DNA (ddRAD) sequencing to analyze samples from 33 tortoises (11 from each main island). Using 5426 variant sites within the tortoise genome, we detected patterns of within-island population structure, but no differentiation between the islands. These unexpected results highlight the importance of using genome-wide genetic markers to capture higher-resolution genetic structure to inform future management plans, even in a seemingly panmictic population. We show that low-coverage ddRAD sequencing provides an affordable alternative approach to conservation genomic projects of non-model species with large genomes.

Kin relationships in cultural species of the marine realm: case study of a matrilineal social group of sperm whales off Mauritius island, Indian Ocean

Understanding the organization and dynamics of social groups of marine mammals through the study of kin relationships is particularly challenging. Here, we studied a stable social group of sperm whales off Mauritius, using underwater observations, individual-specific identification, non-invasive sampling and genetic analyses based on mitochondrial sequencing and microsatellite profiling. Twenty-four sperm whales were sampled between 2017 and 2019. All individuals except one adult female shared the same mitochondrial DNA (mtDNA) haplotype-one that is rare in the western Indian Ocean-thus confirming with near certainty the matrilineality of the group. All probable first- and second-degree kin relationships were depicted in the sperm whale social group: 13 first-degree and 27 second-degree relationships were identified. Notably, we highlight the likely case of an unrelated female having been integrated into a social unit, in that she presented a distinct mtDNA haplotype and no close relationships with any members of the group. Investigating the possible matrilineality of sperm whale cultural units (i.e. vocal clans) is the next step in our research programme to elucidate and better apprehend the complex organization of sperm whale social groups.

Genetic Differentiation of a New World Screwworm Fly Population from Uruguay Detected by SNPs, Mitochondrial DNA and Microsatellites in Two Consecutive Years

The New World screwworm (NWS) fly, Cochliomyia hominivorax (Diptera: Calliphoridae), is an economically important ectoparasite currently distributed in South America and in the Caribbean basin. The successful eradication of this species in USA, Mexico and continental Central America was achieved by a control program based on the sterile insect technique (SIT). In order to implement a genetic control strategy over the NWS fly's current area of occurrence, first, it is necessary to understand the species dynamics and population structure. In order to address this objective, the spatial genetic structure of the NWS fly was previously reported in South America based on different genetic markers; however, to date, no study has investigated temporal changes in the genetic composition of its populations. In the current study, the temporal genetic structure of a NWS fly population from Uruguay was investigated through two consecutive samplings from the same locality over an interval of approximately 18 generations. The genetic structure was accessed with neutral and under selection SNPs obtained with genotyping-by-sequencing. The results gathered with these data were compared to estimates achieved with mitochondrial DNA sequences and eight microsatellite markers. Temporal changes in the genetic composition were revealed by all three molecular markers, which may be attributed to seasonal changes in the NWS fly's southern distribution. SNPs were employed for the first time for estimating the genetic structure in a NWS fly population; these results provide new clues and perspectives on its population genetic structure. This approach could have significant implications for the planning and implementation of management programs.

Exploring variability in the diet of depredating sperm whales in the Gulf of Alaska through stable isotope analysis

Sperm whales interact with commercially important groundfish fisheries offshore in the Gulf of Alaska (GOA). This study aims to use stable isotope analysis to better understand the trophic variability of sperm whales and their potential prey, and to use dietary mixing models to estimate the importance of prey species to sperm whale diets. We analysed tissue samples from sperm whales and seven potential prey (five groundfish and two squid species). Samples were analysed for stable carbon and nitrogen isotope ratios, and diet composition was estimated using Bayesian isotopic mixing models. Mixing model results suggest that an isotopically combined sablefish/dogfish group, skates and rockfish make up the largest proportion of sperm whale diets (35%, 28% and 12%) in the GOA. The top prey items of whales that interact more frequently with fishing vessels consisted of skates (49%) and the sablefish/dogfish group (24%). This is the first known study to provide an isotopic baseline of adult male sperm whales and these adult groundfish and offshore squid species, and to assign contributions of prey to whale diets in the GOA. This study provides information to commercial fishermen and fisheries managers to better understand trophic connections of important commercial species.

Using Noninvasive Genetic Sampling to Survey Rare Butterfly Populations

Advances in nondestructive genetic sampling techniques continue to offer new opportunities for studying organisms, particularly those of conservation concern where more traditional invasive sampling methods are often not available. As part of a proof-of-concept, we investigated the effectiveness of using the chorion from residual butterfly egg debris as a source of viable genetic material for analysis. Laboratory material from a captive breeding population of the federally endangered Miami blue butterfly (Cyclargus thomasi bethunebakeri) was used to test efficacy and refine the methodology. The resulting best practices were subsequently evaluated using field-collected material from extant north Florida populations of the at-risk frosted elfin butterfly (Callophyrs irus). Our results demonstrated that it is possible to extract DNA of sufficiently high quantity and quality for successful gene sequencing. We additionally describe a simple, low-cost, and reliable method of collecting and storing egg debris samples that can be consistently adopted for field or laboratory work as well as deployed with projects that have a larger geographic scope and/or involve citizen scientists. Potential limitations related to field sample collection are discussed as well as needs for future evaluation.

Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin

The southern river terrapin, Batagur affinis is one of the world's 25 most endangered freshwater turtle species. The major portion of the global population is currently found in peninsular Malaysia, with the only remnant Indochinese population in southern Cambodia. For more than a decade, wild nests in this remnant Cambodian population have been fenced and hatchlings reared in captivity. Here we amplified 10 microsatellite markers from all 136 captive individuals, obtained 2,658 presumably unlinked and neutral single nucleotide polymorphisms from 72 samples with ddRAD-seq, and amplified 784 bp of mtDNA from 50 samples. Our results reveal that the last Indochinese population comprised only four kinship groups as of 2012, with all offspring sired from <10 individuals in the wild. We demonstrate an obvious decrease in genetic contributions of breeders in the wild from 2006-2012 and identify high-value breeders instrumental for ex-situ management of the contemporary genetic stock of the species.

Causes and consequences of female centrality in cetacean societies

Cetaceans are fully aquatic predatory mammals that have successfully colonized virtually all marine habitats. Their adaptation to these habitats, so radically different from those of their terrestrial ancestors, can give us comparative insights into the evolution of female roles and kinship in mammalian societies. We provide a review of the diversity of such roles across the Cetacea, which are unified by some key and apparently invariable life-history features. Mothers are uniparous, while paternal care is completely absent as far as we currently know. Maternal input is extensive, lasting months to many years. Hence, female reproductive rates are low, every cetacean calf is a significant investment, and offspring care is central to female fitness. Here strategies diverge, especially between toothed and baleen whales, in terms of mother-calf association and related social structures, which range from ephemeral grouping patterns to stable, multi-level, societies in which social groups are strongly organized around female kinship. Some species exhibit social and/or spatial philopatry in both sexes, a rare phenomenon in vertebrates. Communal care can be vital, especially among deep-diving species, and can be supported by female kinship. Female-based sociality, in its diverse forms, is therefore a prevailing feature of cetacean societies. Beyond the key role in offspring survival, it provides the substrate for significant vertical and horizontal cultural transmission, as well as the only definitive non-human examples of menopause. This article is part of the theme issue 'The evolution of female-biased kinship in humans and other mammals'.

Diet and mitochondrial DNA haplotype of a sperm whale (Physeter macrocephalus) found dead off Jurong Island, Singapore

Despite numerous studies across the large geographic range of the sperm whale (Physeter macrocephalus), little is known about the diet and mitochondrial DNA haplotypes of this strongly female philopatric species in waters off Southeast Asia. A female sperm whale found dead in Singapore waters provided the opportunity to study her diet and mitochondrial DNA haplotype. Here we report on the identification of stomach contents and mitochondrial DNA haplotype of this individual, and we include coastal hydrodynamic modelling to determine the possible geographic origin of the whale. At least 28 species of prey were eaten by this adult female whale, most of which were cephalopods. The mesopelagic squids Taonius pavo, Histioteuthis pacifica, Chiroteuthis imperator,and Ancistrocheirus lesueurii made up over 65% of the whale's stomach contents. Plastic debris was also found in the whale's stomach. Based on the diet, genetics, and coastal hydrodynamic modelling that suggest an easterly drift of the whale carcass over several days, the dead sperm whale in Singapore probably originated from a pod in the Southern Indian Ocean. This study provides an increase in the understanding the diet and natural history of the sperm whale in Southeast Asia. The combined analyses of stomach contents, DNA, and hydrodynamic modeling could provide a context to future studies on the sperm whale strandings, and have broader applicability for other marine mammals in the region.

First genomic study on Lake Tanganyika sprat Stolothrissa tanganicae: a lack of population structure calls for integrated management of this important fisheries target species

BACKGROUND

Clupeid fisheries in Lake Tanganyika (East Africa) provide food for millions of people in one of the world's poorest regions. Due to climate change and overfishing, the clupeid stocks of Lake Tanganyika are declining. We investigate the population structure of the Lake Tanganyika sprat Stolothrissa tanganicae, using for the first time a genomic approach on this species. This is an important step towards knowing if the species should be managed separately or as a single stock. Population structure is important for fisheries management, yet understudied for many African freshwater species. We hypothesize that distinct stocks of S. tanganicae could be present due to the large size of the lake (isolation by distance), limnological variation (adaptive evolution), or past separation of the lake (historical subdivision). On the other hand, high mobility of the species and lack of obvious migration barriers might have resulted in a homogenous population.

RESULTS

We performed a population genetic study on wild-caught S. tanganicae through a combination of mitochondrial genotyping (96 individuals) and RAD sequencing (83 individuals). Samples were collected at five locations along a north-south axis of Lake Tanganyika. The mtDNA data had low global FST and, visualised in a haplotype network, did not show phylogeographic structure. RAD sequencing yielded a panel of 3504 SNPs, with low genetic differentiation (FST = 0.0054; 95% CI: 0.0046-0.0066). PCoA, fineRADstructure and global FST suggest a near-panmictic population. Two distinct groups are apparent in these analyses (FST = 0.1338 95% CI: 0.1239,0.1445), which do not correspond to sampling locations. Autocorrelation analysis showed a slight increase in genetic difference with increasing distance. No outlier loci were detected in the RADseq data.

CONCLUSION

Our results show at most very weak geographical structuring of the stock and do not provide evidence for genetic adaptation to historical or environmental differences over a north-south axis. Based on these results, we advise to manage the stock as one population, integrating one management strategy over the four riparian countries. These results are a first comprehensive study on the population structure of these important fisheries target species, and can guide fisheries management.

Genetic and genomic monitoring with minimally invasive sampling methods

The decreasing cost and increasing scope and power of emerging genomic technologies are reshaping the field of molecular ecology. However, many modern genomic approaches (e.g., RAD-seq) require large amounts of high-quality template DNA. This poses a problem for an active branch of conservation biology: genetic monitoring using minimally invasive sampling (MIS) methods. Without handling or even observing an animal, MIS methods (e.g., collection of hair, skin, faeces) can provide genetic information on individuals or populations. Such samples typically yield low-quality and/or quantities of DNA, restricting the type of molecular methods that can be used. Despite this limitation, genetic monitoring using MIS is an effective tool for estimating population demographic parameters and monitoring genetic diversity in natural populations. Genetic monitoring is likely to become more important in the future as many natural populations are undergoing anthropogenically driven declines, which are unlikely to abate without intensive adaptive management efforts that often include MIS approaches. Here, we profile the expanding suite of genomic methods and platforms compatible with producing genotypes from MIS, considering factors such as development costs and error rates. We evaluate how powerful new approaches will enhance our ability to investigate questions typically answered using genetic monitoring, such as estimating abundance, genetic structure and relatedness. As the field is in a period of unusually rapid transition, we also highlight the importance of legacy data sets and recommend how to address the challenges of moving between traditional and next-generation genetic monitoring platforms. Finally, we consider how genetic monitoring could move beyond genotypes in the future. For example, assessing microbiomes or epigenetic markers could provide a greater understanding of the relationship between individuals and their environment.

Galápagos sperm whales (Physeter macrocephalus): waxing and waning over three decades

While population sizes and structures naturally fluctuate over time, rapid within-generation changes are usually driven by shifts in habitat quality and (or) abrupt mortality. We evaluate how sperm whales (Physeter macrocephalus L., 1758 = Physeter catodon L., 1758) responded to the dynamic habit off the Galápagos Islands over 30 years, relating it to variation in prey availability and whaling operations in the tropical Pacific. In the 1980s, males and females were commonly sighted foraging and socializing in the northwest of the archipelago. Sightings decreased during the 1990s; by the 2000s, they became very rare: occasional single foraging males were sighted and females abandoned the archipelago. In the 2010s, whales return to the southern waters, in large groups with apparently more breeding males and calves. The waxing and waning of Galápagos sperm whales are likely caused by environmental shifts together with ripple effects of whaling. Their patchy prey are influenced by variation in sea temperature and productivity, which drives movements of whales in and out of the archipelago. Whaling may have aggravated these movements by leaving an attractive surplus of prey in coastal waters depleted of whales. These findings highlight the magnitude of spatiotemporal scales used by sperm whales and the consequent challenges of assessing population dynamics of long-lived, mobile pelagic species.

Collateral damage to marine and terrestrial ecosystems from Yankee whaling in the 19th century

Yankee whalers of the 19th century had major impacts on populations of large whales, but these leviathans were not the only taxa targeted. Here, we describe the “collateral damage,” the opportunistic or targeted taking of nongreat whale species by the American whaling industry. Using data from 5,064 records from 79 whaling logs occurring between 1840 and 1901, we show that Yankee whalers captured 5,255 animals across three large ocean basins from 32 different taxonomic categories, including a wide range of marine and terrestrial species. The taxa with the greatest number of individuals captured were walruses (Odobenus rosmarus), ducks (family Anatidae), and cod (Gadus sp.). By biomass, the most captured species were walruses, grampus (a poorly defined group within Odontoceti), and seals (family Otariidae). The whalers captured over 2.4 million kg of nongreat whale meat equaling approximately 34 kg of meat per ship per day at sea. The species and areas targeted shifted over time in response to overexploitation of whale populations, with likely intensive local impacts on terrestrial species associated with multiyear whaling camps. Our results show that the ecosystem impacts of whaling reverberated on both marine and coastal environments.

Structure and Genetic Variability of the Oceanic Whitetip Shark, Carcharhinus longimanus, Determined Using Mitochondrial DNA

Information regarding population structure and genetic connectivity is an important contribution when establishing conservation strategies to manage threatened species. The oceanic whitetip shark, Carcharhinus longimanus, is a highly migratory, large-bodied, pelagic shark listed by the IUCN (International Union for Conservation of Nature) Red List as "vulnerable" throughout its range and "critically endangered" in the western north Atlantic. In 2014, the species was protected globally under Appendix II of CITES (Convention on International Trade in Endangered Species), limiting and regulating trade. This study used partial sequences of mitochondrial DNA (mtDNA) control region to determine the population genetic structure of oceanic whitetip sharks across the Atlantic and Indian Oceans. 724 base pairs were obtained from 215 individuals that identifed nine polymorphic sites and defined 12 distinct haplotypes. Total nucleotide diversity (π) was 0.0013 and haplotype diversity (h) was 0.5953. The Analysis of Molecular Variance (AMOVA) evidenced moderate levels of population structure (ɸST = 0.1039) with restricted gene flow between the western and eastern Atlantic Ocean, and a strong relationship between the latter region and the Indian Ocean. Even though the oceanic whitetip is a highly migratory animal the results presented here show that their genetic variability is slightly below average of other pelagic sharks. Additionally, this study recommends that at least two populations in the Atlantic Ocean should be considered distinct (eastern and western Atlantic) and conservation efforts should be focused in areas with the greatest genetic diversity by environmental managers.

Developing Exon-Primed Intron-Crossing (EPIC) markers for population genetic studies in three Aedes disease vectors

Aedes aegypti, Aedes notoscriptus, and Aedes albopictus are important vectors of many arboviruses implicated in human disease such as dengue fever. Genetic markers applied across vector species can provide important information on population structure, gene flow, insecticide resistance, and taxonomy, however, robust microsatellite markers have proven difficult to develop in these species and mosquitoes generally. Here we consider the utility and transferability of 15 Ribosome protein (Rp) Exon-Primed Intron-Crossing (EPIC) markers for population genetic studies in these 3 Aedes species. Rp EPIC markers designed for Ae. aegypti also successfully amplified populations of the sister species, Ae. albopictus, as well as the distantly related species, Ae. notoscriptus. High SNP and good indel diversity in sequenced alleles plus support for amplification of the same regions across populations and species were additional benefits of these markers. These findings point to the general value of EPIC markers in mosquito population studies.

Carbon and nitrogen isotopes from top predator amino acids reveal rapidly shifting ocean biochemistry in the outer California Current

Climatic variation alters biochemical and ecological processes, but it is difficult both to quantify the magnitude of such changes, and to differentiate long-term shifts from inter-annual variability. Here, we simultaneously quantify decade-scale isotopic variability at the lowest and highest trophic positions in the offshore California Current System (CCS) by measuring δ¹⁵N and δ¹³C values of amino acids in a top predator, the sperm whale (Physeter macrocephalus). Using a time series of skin tissue samples as a biological archive, isotopic records from individual amino acids (AAs) can reveal the proximate factors driving a temporal decline we observed in bulk isotope values (a decline of ≥1 ‰) by decoupling changes in primary producer isotope values from those linked to the trophic position of this toothed whale. A continuous decline in baseline (i.e., primary producer) δ¹⁵N and δ¹³C values was observed from 1993 to 2005 (a decrease of ∼4‰ for δ¹⁵N source-AAs and 3‰ for δ¹³C essential-AAs), while the trophic position of whales was variable over time and it did not exhibit directional trends. The baseline δ¹⁵N and δ¹³C shifts suggest rapid ongoing changes in the carbon and nitrogen biogeochemical cycling in the offshore CCS, potentially occurring at faster rates than long-term shifts observed elsewhere in the Pacific. While the mechanisms forcing these biogeochemical shifts remain to be determined, our data suggest possible links to natural climate variability, and also corresponding shifts in surface nutrient availability. Our study demonstrates that isotopic analysis of individual amino acids from a top marine mammal predator can be a powerful new approach to reconstructing temporal variation in both biochemical cycling and trophic structure.

Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs

High-density SNP arrays developed for humans and their companion species provide a rapid and convenient tool for generating SNP data in closely-related non-model organisms, but have not yet been widely applied to phylogenetically divergent taxa. Consequently, we used the CanineHD BeadChip to genotype 24 Antarctic fur seal (Arctocephalus gazella) individuals. Despite seals and dogs having diverged around 44 million years ago, 33,324 out of 173,662 loci (19.2%) could be genotyped, of which 173 were polymorphic and clearly interpretable. Two SNPs were validated using KASP genotyping assays, with the resulting genotypes being 100% concordant with those obtained from the high-density array. Two loci were also confirmed through in silico visualisation after mapping them to the fur seal transcriptome. Polymorphic SNPs were distributed broadly throughout the dog genome and did not differ significantly in proximity to genes from either monomorphic SNPs or those that failed to cross-amplify in seals. However, the nearest genes to polymorphic SNPs were significantly enriched for functional annotations relating to energy metabolism, suggesting a possible bias towards conserved regions of the genome.

Low diversity in the mitogenome of sperm whales revealed by next-generation sequencing

Large population sizes and global distributions generally associate with high mitochondrial DNA control region (CR) diversity. The sperm whale (Physeter macrocephalus) is an exception, showing low CR diversity relative to other cetaceans; however, diversity levels throughout the remainder of the sperm whale mitogenome are unknown. We sequenced 20 mitogenomes from 17 sperm whales representative of worldwide diversity using Next Generation Sequencing (NGS) technologies (Illumina GAIIx, Roche 454 GS Junior). Resequencing of three individuals with both NGS platforms and partial Sanger sequencing showed low discrepancy rates (454-Illumina: 0.0071%; Sanger-Illumina: 0.0034%; and Sanger-454: 0.0023%) confirming suitability of both NGS platforms for investigating low mitogenomic diversity. Using the 17 sperm whale mitogenomes in a phylogenetic reconstruction with 41 other species, including 11 new dolphin mitogenomes, we tested two hypotheses for the low CR diversity. First, the hypothesis that CR-specific constraints have reduced diversity solely in the CR was rejected as diversity was low throughout the mitogenome, not just in the CR (overall diversity π = 0.096%; protein-coding 3rd codon = 0.22%; CR = 0.35%), and CR phylogenetic signal was congruent with protein-coding regions. Second, the hypothesis that slow substitution rates reduced diversity throughout the sperm whale mitogenome was rejected as sperm whales had significantly higher rates of CR evolution and no evidence of slow coding region evolution relative to other cetaceans. The estimated time to most recent common ancestor for sperm whale mitogenomes was 72,800 to 137,400 years ago (95% highest probability density interval), consistent with previous hypotheses of a bottleneck or selective sweep as likely causes of low mitogenome diversity.

Single nucleotide polymorphism discovery in albacore and Atlantic bluefin tuna provides insights into worldwide population structure

The optimal management of the commercially important, but mostly over-exploited, pelagic tunas, albacore (Thunnus alalunga Bonn., 1788) and Atlantic bluefin tuna (BFT; Thunnus thynnus L., 1758), requires a better understanding of population structure than has been provided by previous molecular methods. Despite numerous studies of both species, their population structures remain controversial. This study reports the development of single nucleotide polymorphisms (SNPs) in albacore and BFT and the application of these SNPs to survey genetic variability across the geographic ranges of these tunas. A total of 616 SNPs were discovered in 35 albacore tuna by comparing sequences of 54 nuclear DNA fragments. A panel of 53 SNPs yielded FST values ranging from 0.0 to 0.050 between samples after genotyping 460 albacore collected throughout the distribution of this species. No significant heterogeneity was detected within oceans, but between-ocean comparisons (Atlantic, Pacific and Indian oceans along with Mediterranean Sea) were significant. Additionally, a 17-SNP panel was developed in Atlantic BFT by cross-species amplification in 107 fish. This limited number of SNPs discriminated between samples from the two major spawning areas of Atlantic BFT (FST  = 0.116). The SNP markers developed in this study can be used to genotype large numbers of fish without the need for standardizing alleles among laboratories.

Using pedigree reconstruction to estimate population size: genotypes are more than individually unique marks

Estimates of population size are critical for conservation and management, but accurate estimates are difficult to obtain for many species. Noninvasive genetic methods are increasingly used to estimate population size, particularly in elusive species such as large carnivores, which are difficult to count by most other methods. In most such studies, genotypes are treated simply as unique individual identifiers. Here, we develop a new estimator of population size based on pedigree reconstruction. The estimator accounts for individuals that were directly sampled, individuals that were not sampled but whose genotype could be inferred by pedigree reconstruction, and individuals that were not detected by either of these methods. Monte Carlo simulations show that the population estimate is unbiased and precise if sampling is of sufficient intensity and duration. Simulations also identified sampling conditions that can cause the method to overestimate or underestimate true population size; we present and discuss methods to correct these potential biases. The method detected 2–21% more individuals than were directly sampled across a broad range of simulated sampling schemes. Genotypes are more than unique identifiers, and the information about relationships in a set of genotypes can improve estimates of population size.

Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms

Knowledge about population structure and connectivity of waterfowl species, especially mallards (Anas platyrhynchos), is a priority because of recent outbreaks of avian influenza. Ringing studies that trace large-scale movement patterns have to date been unable to detect clearly delineated mallard populations. We employed 363 single nucleotide polymorphism markers in combination with population genetics and phylogeographical approaches to conduct a population genomic test of panmixia in 801 mallards from 45 locations worldwide. Basic population genetic and phylogenetic methods suggest no or very little population structure on continental scales. Nor could individual-based structuring algorithms discern geographical structuring. Model-based coalescent analyses for testing models of population structure pointed to strong genetic connectivity among the world's mallard population. These diverse approaches all support the conclusion that there is a lack of clear population structure, suggesting that the world's mallards, perhaps with minor exceptions, form a single large, mainly interbreeding population.

Multiple SNP markers reveal fine-scale population and deep phylogeographic structure in European anchovy (Engraulis encrasicolus L.)

Geographic surveys of allozymes, microsatellites, nuclear DNA (nDNA) and mitochondrial DNA (mtDNA) have detected several genetic subdivisions among European anchovy populations. However, these studies have been limited in their power to detect some aspects of population structure by the use of a single or a few molecular markers, or by limited geographic sampling. We use a multi-marker approach, 47 nDNA and 15 mtDNA single nucleotide polymorphisms (SNPs), to analyze 626 European anchovies from the whole range of the species to resolve shallow and deep levels of population structure. Nuclear SNPs define 10 genetic entities within two larger genetically distinctive groups associated with oceanic variables and different life-history traits. MtDNA SNPs define two deep phylogroups that reflect ancient dispersals and colonizations. These markers define two ecological groups. One major group of Iberian-Atlantic populations is associated with upwelling areas on narrow continental shelves and includes populations spawning and overwintering in coastal areas. A second major group includes northern populations in the North East (NE) Atlantic (including the Bay of Biscay) and the Mediterranean and is associated with wide continental shelves with local larval retention currents. This group tends to spawn and overwinter in oceanic areas. These two groups encompass ten populations that differ from previously defined management stocks in the Alboran Sea, Iberian-Atlantic and Bay of Biscay regions. In addition, a new North Sea-English Channel stock is defined. SNPs indicate that some populations in the Bay of Biscay are genetically closer to North Western (NW) Mediterranean populations than to other populations in the NE Atlantic, likely due to colonizations of the Bay of Biscay and NW Mediterranean by migrants from a common ancestral population. Northern NE Atlantic populations were subsequently established by migrants from the Bay of Biscay. Populations along the Iberian-Atlantic coast appear to have been founded by secondary waves of migrants from a southern refuge.

Can genetic differences explain vocal dialect variation in sperm whales, Physeter macrocephalus?

Sperm whale social groups can be assigned to vocal clans based on their production of codas, short stereotyped patterns of clicks. It is currently unclear whether genetic variation could account for these behavioural differences. We studied mitochondrial DNA (mtDNA) variation among sympatric vocal clans in the Pacific Ocean, using sequences extracted from sloughed skin samples. We sampled 194 individuals from 30 social groups belonging to one of three vocal clans. As in previous studies of sperm whales, mtDNA control region diversity was low (π = 0.003), with just 14 haplotypes present in our sample. Both hierarchical AMOVAs and partial Mantel tests showed that vocal clan was a more important factor in matrilineal population genetic structure than geography, even though our sampling spanned thousands of kilometres. The variance component attributed to vocal dialects (7.7%) was an order of magnitude higher than those previously reported in birds, while the variance component attributed to geographic area was negligible. Despite this, the two most common haplotypes were present in significant quantities in each clan, meaning that variation in the control region cannot account for behavioural variation between clans, and instead parallels the situation in humans where parent-offspring transmission of language variation has resulted in correlations with neutral genes. Our results also raise questions for the management of sperm whale populations, which has traditionally been based on dividing populations into geographic 'stocks', suggesting that culturally-defined vocal clans may be more appropriate management units.